The ultrasonic cell disruption method was used to efficiently extract isothiocyanates and other volatile compounds from radish microgreens. A total of 51 volatiles were identified and quantified by headspace solid-phase micro-extraction and gas chromatography–mass spectrometry (HS-SPME/GC–MS) in four radish microgreen cultivars, mainly including alcohols, aldehydes, isothiocyanates, sulfides, ketones, esters, terpenes, and hydrocarbons. The correlation between cultivars and volatile compounds was determined by chemometrics analysis, including principal component analysis (PCA) and hierarchical clustering heat maps. The aroma profiles were distinguished based on the odor activity value (OAV), odor contribution rate (OCR), and radar fingerprint chart (RFC) of volatile compounds. This study not only revealed the different flavor characteristics in four cultivars but also established a theoretical basis for the genetic improvement of radish microgreen flavors.